Vibrational spectroscopic studies of the interaction of water with serine

The vibrational dynamics of water around serine was investigated by using Raman spectroscopy and inelastic incoherent neutron scattering. Experiments with serine in deuterium oxide were performed to assist the assignment. The study shows that for the serine, the exchange of protons-deuterons on the active -NH3+ and -OH groups were relatively easy, whereas there were hardly any exchanged on the -CH or -CH2- groups. The main features of the spectra for hydrated samples (versus the dry samples) were altered considerably; new sharp peaks in the measured spectra appeared, indicating that the hydrogen bonding between water and serine had disturbed the structure of the serine molecule.     

基于金银纳米立方体构建高灵敏CA-153传感器的研究

癌抗原-153(CA-153)是乳腺癌最重要的特异性标志物。利用CA-153与其抗体之间的特异性识别性构建"三明治"夹心结构的免疫传感器,在玻碳电极上修饰金纳米/氧化石墨烯复合材料,通过纳米金和CA-153抗体之间的吸附作用,将抗体固定于电极表面,以牛血清白蛋白封闭非特异性吸附位点。金银(AuAg)纳米立方体标记CA-153二抗,标记的AuAg纳米立方体催化过氧化氢氧化电子媒介体硫堇,采用差分脉冲伏安法检测CA-153的电化学信号。在最优条件下,此传感器的响应电流与CA-153浓度的对数在2.0×10~(-5)~100 U/mL范围内呈良好的线性关系,检出限(S/N=3)为7.0×10~(-6)U/mL。对实际血清样品进行加标回收实验,回收率为92.2%~110.2%,相对标准偏差不大于8.7%。     

Serine protease inhibition by a silanediol peptidomimetic

Silanediol peptidomimetics are demonstrated to inhibit a serine protease. Asymmetric synthesis of the inhibitor was accomplished using Brown hydroboration and CBS reduction of an acylsilane intermediate. The silanediol product was found to inhibit the serine protease chymotrypsin with a K(i) of 107 nM. Inhibition of the enzyme may involve exchange of a silane hydroxyl with the active site serine nucleophile, contrasting with previous silanediol protease inhibitors.     

A new mechanism of acyl group transfer in the reaction catalyzed by D-glyceraldehyde-3-phosphate dehydrogenase

D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12) catalyzes the oxidative phosphorylation of its substrate in a two-step reaction. Asa result of the first, oxidativestep, the covalent intermediate where in 3-phosphoglyceroyl moiety is bound to Cys149 of the active center is subjected to nucleophilic attack by inorganic phosphate, but remains resistant to hydrolytic decomposition. This ensures tight coupling of oxidation with phosphorylation in glycolysis. In this article, we present the experimental evidence for the conversion of GAPDH into a form capable of performing the reaction in the absence of inorganic phosphate. The structural basis for this conversion is the oxidation of a cysteine residue (probably Cys 153) into a sulfenic acid derivative under mild conditions to affect the integrity of the essential Cys 149. As a result, an intram olecular transfer of 3-phosphoglyceroyl group from the active center Cys 149 to Cys 153 becomes possible with subsequent hydrolysis of the sulfenyl carboxylate intermediate.     

Preparation of samarium-153-EDTMP and determination of its radiochemical purity using paper chromatography

Samarium-153-ethylenediaminetetramethylenephosphonate (¹⁵³Sm-EDTMP) has been used to palliate pain resulting from bone cancer. This paper describes the preparation of¹⁵³SmCl₃ from irradiated natural samarium and the ability of¹⁵³Sm to complex with EDTMP in liquid and in freeze-dried forms. The evaluation of radiolabeled EDTMP was done by paper chromatography. A rapid evaluation of free¹⁵³SmCl₃ and¹⁵³Sm-EDTMP was developed using a miniaturized chromatographic system.     

Low-Energy Electron Attachment to Serine Conformers: Shape Resonances and Dissociation Dynamics

Shape resonances of electron-molecule system formed in the low-energy electron attachment to four low-lying conformers of serine (serine 1, serine 2, serine 3, and serine 4) in gas phase are investigated using the quantum scattering method with the non-empirical model potentials in single-center expansion. In the attachment energy range of 0-10 eV, three shape resonances for serine 1, serine 2, and serine 4 and four shape resonances for serine 3 are predicted. The one-dimensional potential energy curves of the temporary negative ions of electron-serine are calculated to explore the correlations between the shape resonance and the bond cleavage. The bond-cleavage selectivity of the different resonant states for a certain conformer is demonstrated, and the recent experimental results about the dissociative electron attachment to serine are interpreted on the basis of present calculations.     

Dynamic kinetic resolution of racemic beta-haloalcohols: direct access to enantioenriched epoxides

The direct chemo-enzymatic DKR of racemic beta-haloalcohols is reported, yielding the corresponding optically active epoxides in a single step. The mutant haloalcohol dehalogenase HheC Cys153Ser Trp249Phe is used for the asymmetric ring closure, whereas racemization of the remaining enantiomer of the haloalcohol is achieved using the new iridacycle 3, one of the most effective racemization catalysts to date for beta-haloalcohols.     

Chiral enrichment of serine via formation,dissociation, and soft-landing of octameric cluster ions

Chiral enrichment of serine is achieved in experiments that involve formation of serine octamers starting from non-racemic serine solutions. Serine octamers were generated by means of electrospray and sonic spray ionization of aqueous solutions of d(3)-L-serine (108 Da) and D-serine (105 Da) having different molar ratios of enantiomers. A cyclic process involving the formation of chirally-enriched octameric cluster ions and their dissociation, viz. Ser(1) --> Ser(8) --> Ser(1), allows serine monomers to be regenerated with increased enantiomeric excess as shown in two types of experiments: (1) Chiral enrichment in serine was observed in MS/MS/MS experiments in a quadrupole ion trap in which the entire distribution of serine octamers formed from non-racemic solutions was isolated, collisionally activated, and fragmented. Monomeric serine was regenerated with increased enantiomeric excess upon dissociation of octamers when compared with the enantiomeric composition of the original solution. (2) Chiral enrichment was observed in the products of soft-landing of mass-selected protonated serine octamers. These ions were generated by means of electrospray or sonic spray ionization, mass selected, and collected on a gold surface using ion soft-landing. Chiral enrichment of the soft-landed serine was established by redissolving the recovered material and comparing the intensities of protonated molecular ions of d(3)-L-serine and D-serine after APCI-MS analysis. Both of these experiments showed comparable results, suggesting that formation of serine octamers depends only on the enantiomeric composition of the serine solution and that the magnitude of the chiral preference is intrinsic to octamers formed from solutions of given chiral composition.     

Acylation versus sulfonylation in the inhibition of elastase by 3-oxo-beta-sultams

beta-Sultams are the sulfonyl analogues of beta-lactams, and 3-oxo-beta-sultams are both beta-lactams and beta-sultams and, therefore, susceptible to nucleophilic attack at either the acyl or the sulfonyl center. They are novel inactivators of serine enzymes. The second-order rate constant for the inactivation of elastase at pH 6 by N-benzyl-4,4-dimethyl-3-oxo-beta-sultam is 768 M-1 s-1, which is 103-fold greater than that with N-benzoyl beta-sultam. However, in contrast to N-acyl beta-sultams, which sulfonylate the active site serine residue to form a sulfonate ester, 3-oxo-beta-sultams inhibit the enzyme by acylation followed by slow deacylation to regenerate the active enzyme.     

Selective and diagnostic labelling of serine hydrolases with reactive phosphonate inhibitors

Reactive phosphonates are important probes to target the active site of serine hydrolases, one of the largest and most diverse family of enzymes. Developing such inhibitory probes is of special importance in activity based protein profiling, a strategy that is increasingly used to gain information about a certain class of enzymes in complex proteosomes. Therefore, gaining detailed information about these inhibition events on the individual protein level is important since it affords information that can be used to fine-tune the probe for a specific task. Here, we report a novel and versatile synthesis protocol to access a variety of functionalised p-nitrophenyl phosphonate (PNPP) inhibitors from a common azide functionalised precursor using click chemistry. The obtained PNPPs were successfully used to covalently label serine hydrolases in their active sites with molecular tags. Furthermore, a model study is described in which we developed straightforward protocols that can be used to study protein inhibition events. Kinetic studies using UV-Vis and fluorescence spectroscopy techniques revealed that these PNPPs possess different inhibition rates for various proteins and were shown to be suitable probes to discriminate between various lipases. Additionally, we demonstrate that PNPPs are highly selective for serine hydrolases, making these probes very interesting as diagnostic or affinity probes for studying proteins in complex proteosomes.     

Qualitative analysis of the fluorophosphonate-based chemical probes using the serine hydrolases from mouse liver and poly-3-hydroxybutyrate depolymerase (PhaZ) from Bacillus thuringiensis

The serine hydrolase family consists of more than 200 members and is one of the largest enzyme families in the human genome. Although up to 50?% of this family remains unannotated, there are increasing evidences that activities of certain serine hydrolases are associated with diseases like cancer neoplasia, invasiveness, etc. By now, several activity-based chemical probes have been developed and are applied to profile the global activity of serine hydrolases in diverse proteomes. In this study, two fluorophosphonate (FP)-based chemical probes were synthesized. Further examination of their abilities to label and pull down serine hydrolases was conducted. In addition, the poly-3-hydroxybutyrate depolymerase (PhaZ) from Bacillus thuringiensis was demonstrated as an appropriate standard serine hydrolase, which can be applied to measure the labeling ability and pull-down efficiency of FP-based probes. Furthermore, mass spectrometry (MS) was used to identify the serine residue that covalently bonded to the active probes. Finally, these FP-based probes were shown capable of establishing the serine hydrolase profiles in diverse mouse tissues; the serine hydrolases pulled down from mouse liver organ were further identified by MS. In summary, our study provides an adequate method to evaluate the reactivity of FP-based probes targeting serine hydrolases.

Investigation of a general base mechanism for ester hydrolysis in C-C hydrolase enzymes of the alpha/beta-hydrolase superfamily: a novel mechanism for the serine catalytic triad

Previous mechanistic and crystallographic studies on two C-C hydrolase enzymes, Escherichia coli MhpC and Burkholderia xenovorans BphD, support a general base mechanism for C-C hydrolytic cleavage, rather than the nucleophilic mechanism expected for a serine hydrolase. The role of the active site serine residue could be to form a hydrogen bond with a gem-diolate intermediate, or to protonate such an intermediate. Hydrolase BphD is able to catalyse the hydrolysis of p-nitrophenyl benzoate ester substrates, which has enabled an investigation of these mechanisms using a Hammett analysis, and comparative studies upon five serine esterases and lipases from the alpha/beta-hydrolase family. A reaction parameter (rho) value of +0.98 was measured for BphD-catalysed ester hydrolysis, implying a build-up of negative charge in the transition state, consistent with a general base mechanism. Values of +0.31-0.61 were measured for other serine esterases and lipases, for the same series of esterase substrates. Pre-steady state kinetic studies of ester hydrolysis, using p-nitrophenyl acetate as the substrate, revealed a single step kinetic mechanism for BphD-catalysed ester hydrolysis, with no burst kinetics. A general base mechanism for BphD-catalysed ester hydrolysis is proposed, in which Ser-112 stabilises an oxyanion intermediate through hydrogen bonding, and assists the rotation of this oxyanion intermediate via proton transfer, a novel reaction mechanism for the serine catalytic triad.     

Cystatins, serpins and other families of protease inhibitors in plants

Plant protease inhibitors (PIs) are generally small proteins present in high concentrations in storage tissues (tubers and seeds), and to a lower level in leaves. Even if most of them are active against serine and cysteine proteases, PIs active against aspartic proteases and carboxypeptidases have also been identified. Inhibitors of serine proteases are further classifiable in several families on the basis of their structural features. They comprise the families known as Bowman-Birk, Kunitz, Potato I and Potato II, which are the subject of review articles included in this special issue. In the present article we aim to give an overview of other families of plant PIs, active either against serine proteases or other class of proteases, describing their distribution, activity and main structural characteristics.     

Studies on the Solvation Dynamics of Coumarin 153 in 1‐Ethyl‐3‐Methylimidazolium Alkylsulfate Ionic Liquids: Dependence on Alkyl Chain Length

Steady‐state and time‐resolved fluorescence behavior of coumarin 153 (C153) is investigated in a series of 1‐ethyl‐3‐methylimidazolium alkylsulfate ([C₂mim][C_nOSO₃]) ionic liquids differing only in the length of the linear alkyl chain (n=4, 6, and 8) in the anion. The aim of the present study is to understand the role of alkyl chain length in solute rotation and solvation dynamics of C153 in these ionic liquids. The blueshift observed in the steady‐state absorption and emission maxima of C153 on going from the C₄OSO₃ to the C₈OSO₃ system indicates increasing nonpolar character of the microenvironment of the solute with increasing length of the alkyl side chain of the anion of the ionic liquids. The average solvation time is also found to increase on changing the substituent from butyl to octyl, and this is attributed to the increase in the bulk viscosity of the ILs. A steady blueshift of the time‐zero maximum of the fluorescence spectrum with increasing alkyl chain length also indicates that the probe molecule experiences a less polar environment in the early part of the dynamics. Rotational dynamics of C153 are also analyzed by using the Stokes–Einstein–Debye (SED), Gierer–Wirtz (GW), and Dote–Kivelson–Schwartz (DKS) theories. Analyses of the results seem to suggest decoupling of the rotational motion of the probe from solvent viscosity.     

同位素稀释-高分辨气相色谱/高分辨质谱法测定大气中多溴联苯醚和多溴联苯153

针对环境监测的特点和要求,建立了同位素稀释-高分辨气相色谱/高分辨质谱测定大气中多溴联苯醚(PBDEs)和多溴联苯153(BB153)的方法。采用正己烷/二氯甲烷(1:1, v/v)及正己烷分别对PBDEs和BB153进行快速溶剂萃取,并通过复合硅胶柱净化。在校准曲线最高浓度的10%和90%加标水平下得到的天然内标的平均回收率分别为100%和104%,平均相对标准偏差(n=7)分别为5%和6%;二至十溴代联苯醚和BB153相应的¹³C同位素标准物质回收率在36.5%~133%之间;而一溴代联苯醚¹³C同位素标准物质回收率较差,可能是由于物化性质与其他化合物不同。在实际采样体积为300 m³的情况下,未发生污染物穿透现象;分析物检出限低于2×10^-4 ng/Nm³,提取内标回收率在56%~126%之间(一溴代联苯醚除外)。实验结果表明该方法能对化合物准确定量,适用于大气中二至十溴代联苯醚和BB153的分析。     

Facile synthesis of unusual glycosyl carbamates and amino acid glycosides from propargyl 1,2-orthoesters as glycosyl donors

Propargyl 1,2-O-orthoesters are exploited for the synthesis of 1,2-trans O-glycosides of protected amino acids. N-Fmoc- and N-Cbz protected serine/threonine - benzyl/methyl esters reacted well with glucosyl-, galactosyl-, mannosyl- and lactosyl- derived propargyl 1,2-orthoesters affording respective 1,2-trans glycosides in good yields under AuBr(3)/4 ? MS Powder/CH(2)Cl(2)/rt. t-Boc serine derivative gave serine 1,2-orthoester and glycosyl carbamate. Optimized conditions enabled preparation of new glycosyl carbamates from N-Boc protected amines in a single step using gold catalysts and propargyl 1,2-orthoesters in excellent yields.     

The complex of apomyoglobin with the fluorescent dye coumarin 153

Understanding a protein's dielectric response requires both a theoretical model and a well-defined experimental system. The former has already been proposed by Song (J. Chem. Phys. 116, 9359 [2002]). We suggest that the latter is provided by the complex of coumarin 153 (C153) with apomyoglobin (ApoMb). C153 has been exhaustively studied and has proven to be an excellent probe of the solvation dynamics of polar solvents. Myoglobin is one of the most thoroughly studied proteins. Myoglobins from a wide range of species have been subject to X-ray structural analysis and site-directed mutagenesis. Here, we demonstrate the existence of a robust C153-apomyglobin system by means of molecular dynamics simulations, equilibrium binding studies using a Job's plot and capillary electrophoresis, circular dichroism and time-resolved fluorescence. The reorganization energy of C153 bound to ApoMb is compared with that of C153 in bulk solvent using the method of Jordanides et al. (J. Phys. Chem. B 103, 7995 [1999]).     

Arthrichitin. A New Cell Wall Active Metabolite from Arthrinium phaeospermum

Arthrichitin (1), C(33)H(46)N(4)O(9), is a new cell wall active depsipeptide isolated from the fermentation broth of Arthrinium phaeospermum (HIL Y-903022). Its structure was elucidated on the basis of spectroscopic and chemical degradation studies. Arthrichitin consists of serine, beta-keto tryptophan, glutamic acid, and 2,4-dimethyl-3-hydroxydodecanoic acid units.     

A light-activated probe of intracellular protein kinase activity

The first example of a photoactivated probe of intracellular enzymatic activity is described. The caged derivative of a fluorescent protein kinase C peptide-based sensor was prepared by modifying the free hydroxyl group of a phosphorylatable serine moiety with a photolabile appendage that blocks phosphoryl transfer. We have demonstrated that the caged sensor allows one to (1) sample PKC activity with exquisite temporal precision, (2) control the relative amount of active sensor available for phosphorylation, and (3) examine protein kinase activity at multiple time points.